`dimGenePlot3D`¶

dimGenePlot3D

Description¶

Visualize cells and gene expression according to dimension reduction coordinates

Usage¶

dimGenePlot3D(
  gobject,
  expression_values = c("normalized", "scaled", "custom"),
  genes = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  dim3_to_use = 3,
  show_NN_network = F,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  network_color = "lightgray",
  cluster_column = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  edge_alpha = NULL,
  point_size = 2,
  genes_high_color = NULL,
  genes_mid_color = "white",
  genes_low_color = "blue",
  show_legend = T,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "dimGenePlot3D"
)

Arguments¶

Argument	Description
`gobject`	giotto object
`expression_values`	gene expression values to use
`genes`	genes to show
`dim_reduction_to_use`	dimension reduction to use
`dim_reduction_name`	dimension reduction name
`dim1_to_use`	dimension to use on x-axis
`dim2_to_use`	dimension to use on y-axis
`dim3_to_use`	dimension to use on z-axis
`show_NN_network`	show underlying NN network
`nn_network_to_use`	type of NN network to use (kNN vs sNN)
`network_name`	name of NN network to use, if show_NN_network = TRUE
`network_color`	color of NN network
`cluster_column`	cluster column to select groups
`select_cell_groups`	select subset of cells/clusters based on cell_color parameter
`select_cells`	select subset of cells based on cell IDs
`show_other_cells`	display not selected cells
`other_cell_color`	color of not selected cells
`other_point_size`	size of not selected cells
`edge_alpha`	column to use for alpha of the edges
`point_size`	size of point (cell)
`genes_high_color`	color for high expression levels
`genes_mid_color`	color for medium expression levels
`genes_low_color`	color for low expression levels
`show_legend`	show legend
`show_plot`	show plots
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Details¶

Description of parameters.

Value¶

ggplot

Seealso¶

Other dimension reduction gene expression visualizations:: ``dimGenePlot2D` <#dimgeneplot2d>`_ , ``dimGenePlot` <#dimgeneplot>`_